The homeobox gene goosecoid marks the Spemann organizer in vertebrate gastrula embryos, and is expressed in the craniofacial region, body wall and limbs during organogenesis. Mouse mutants of goosecoid displayed a variety of phenotypes related to the expression pattern at mid-embryogenesis. These defects included loss of the tympanic ring and malformation of the malleus, phenotypes which were reminiscent of the teratogenic effects of retinoic acid (RA). Here we investigated the correlation of goosecoid gene expression and RA-teratogenicity following treatment of mouse embryos in vivo at embryonic day (E) 8 + 5 h. We found that goosecoid was specifically affected at E10.5 in branchial arches I and II. Expression was either reduced to background levels or restricted to the branchial cleft region. This change in goosecoid gene expression correlated with a loss of middle ear ossicles and a partial or complete deletion of the tympanic ring, suggesting a role for goosecoid in executing the RA teratogenic effects.